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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2qan:A2016, See in JSmolMgRNA representative site for type 2PO-2BO Click on the image to toggle views


Site type: 2Pout·2Bout

Schematic drawing for
2Pout·2Bout
MgRNA type 2PO-2BO
List of all 453 Mg2+ binding sites with the site type 2Pout·2Bout in RNA crystal structures in the full dataset (switch to benchmark dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "benchmark dataset", "Coordination Number", "Qv #", "Qs #", "Qe #", "PDB ID" or "Mg2+ ID"
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Mg2+ ion Site type Validation parameters
PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset
4tp6 A1606 2Pout·2Bout 6  0.74  1.00  0.96yes
3v25 A3303 2Pout·2Bout 5  0.62  0.79  0.96yes
4qcx A3441 2Pout·2Bout 2  0.25  0.28  0.96no
3v25 A3269 2Pout·2Bout 4  0.51  0.96  0.96yes
3og0 A2920 2Pout·2Bout 6  0.75  1.00  0.96yes
3ofq A2922 2Pout·2Bout 6  0.75  1.00  0.96yes
3v2d A3306 2Pout·2Bout 5  0.64  0.74  0.96yes
2qan A2340 2Pout·2Bout 5  0.81  0.80  0.97yes
3oaq A1 2Pout·2Bout 6  0.75  0.99  0.97yes
3v28 A1722 2Pout·2Bout 6  0.74  0.98  0.97yes
4qct A3345 2Pout·2Bout 4  0.50  0.64  0.97yes
4dhc B211 2Pout·2Bout 3  0.39  0.64  0.97no
4kiz A3131 2Pout·2Bout 3  0.48  0.21  0.97no
4qcs A3112 2Pout·2Bout 2  0.25  0.29  0.98no
4qcm A1745 2Pout·2Bout 6  0.76  0.99  0.98yes
2z4m A1600 2Pout·2Bout 5  0.81  0.80  0.98yes
4too A3115 2Pout·2Bout 4  0.67  0.65  0.98yes
4nvy A3144 2Pout·2Bout 3  0.38  0.40  0.98no
3dil A229 2Pout·2Bout 5  0.58  0.84  0.98yes
3p49 A738 2Pout·2Bout 4  0.50  0.98  0.99yes
4nvv A3404 2Pout·2Bout 5  0.64  0.80  0.99yes
4nvw A3149 2Pout·2Bout 3  0.37  0.67  0.99no
4nvz B3013 2Pout·2Bout 3  0.38  0.41  0.99no
4qcq A3145 2Pout·2Bout 6  0.76  0.99  0.99yes
3ofx A1 2Pout·2Bout 6  0.75  0.99  0.99yes

# Validation parameters Qv, Qs, Qe are defined in the range of 0 to 1, with 0 indicating poorest reliability and higher value indicating a more reliable site
Qv measures the agreement of the inner-sphere bond valence summation with the oxidation state of Mg2+ (+2)
Qs measures the geometrical symmetry of the ligands distribution around the Mg2+ required for octahedral geometry
Qe measures the agreement of the isotropic atomic displacement (B) factor and occupancy of the Mg2+ compared to those of all atoms in its environment

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations
used for Mg2+
"Site type"		 Mg2+ inner-sphere ligands Geometry for inner-sphere OP Mg2+ outer-sphere moieties
Oph phosphate oxygen (OP1/OP2)
Or ribose oxygen (O2'/O4')
     or oxygen bridging phosphate and ribose (O3'/O5')
Ob nucleobase oxygen      Nb nucleobase nitrogen 		cis- two OP ligands adopt cis- isoform
trans- two OP ligands adopt trans- isoform
fac- three OP ligands adopt fac- isoform
mer- three OP ligands adopt mer- isoform 		Pout phosphate moiety
Rout ribose moiety
Bout nucleobase moiety
Reference: Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>